Gnuplot?
I don't recall it being too bad at hundreds or thousands of points, but it's been a while since I used it (namely in conjunction with Octave).
Could even go worse than a thin JS + HTML Canvas parser/viewer in a browser, assuming network availability (or suitable environment including DOM graphics and file system access). Some thousands of points should be effortless, more if you can do it by GPU assistance (at some level of scaling, WASM + WebGL would probably be warranted, or just do it native with C/++/#, SIMD optimizations, and GDI/DirectX/OpenGL output.
Or since it sounds very logic-analyzery, can you just hijack an existing one? Saleae performs very nicely with millions of points. If the file format is documented, I'd give that a serious look.
Tim